Scripts and information on the figures and graphs presented in the datapaper Atlantic-Camtraps.
V.0. by Renata Muylaert.
data <- read.csv(here("data", "splist_filtered_2017_04d24.csv"), sep = ",")
ef <- read.csv(here("data", "effort.txt"), sep="\t")
View(data)
data <- data[order(data$fo),]
str(data)
unique(data$sp_id)
head(data)
Generated in ArcGis by Fernando Lima.
Fig.
1. Distribution of the camera trap surveys of medium and large
terrestrial mammal communities within the Atlantic Forest extent. Gray
shows the Atlantic Forest extent with remaining forest patches in green
(sensu Ribeiro et. al., 2009). Blue dots show the geographic
locations of studies.
This figure was generated in MS Excel using the sunburst
function.
Fig. 2. Taxonomic information levels of medium and large terrestrial mammal species recorded in camera trap surveys within the Atlantic Forest. Only species considered well detected by camera traps are listed. From the 83 species reported in the database, 8 are not listed because the identification is at genera level. Another 28 species are not listed because they were considered opportunistic records of species not usually detected by camera traps (primates, bats, small rodents, and small marsupials).
fct_rev(fct_infreq(factor(data$species.1)))
[1] Mazama americana Mazama gouazoubira Mazama nana
[4] Sus scrofa Pecari tajacu Tayassu pecari
[7] Canis familiaris Cerdocyon thous Chrysocyon brachyurus
[10] Lycalopex gymnocercus Speothos venaticus Felis catus
[13] Leopardus pardalis Leopardus guttulus Leopardus wiedii
[16] Panthera onca Puma concolor Puma yagouaroundi
[19] Conepatus chinga Conepatus semistriatus Eira barbara
[22] Galictis cuja Lontra longicaudis Nasua nasua
[25] Potos flavus Procyon cancrivorus Cabassous tatouay
[28] Cabassous unicinctus Dasypus novemcinctus Dasypus septemcinctus
[31] Euphractus sexcinctus Priodontes maximus Didelphis albiventris
[34] Didelphis aurita Lepus europaeus Sylvilagus brasiliensis
[37] Tapirus terrestris Myrmecophaga tridactyla Tamandua tetradactyla
[40] Hydrochoerus hydrochaeris Cuniculus paca Dasyprocta azarae
[43] Dasyprocta leporina Chaetomys subspinosus Coendou prehensilis
[46] Sphiggurus insidiosus Sphiggurus villosus
47 Levels: Tayassu pecari Tapirus terrestris ... Cabassous tatouay
colnames(data)[3] <- paste("Order")
p <- ggplot(data, aes(x=reorder(species.1,-fo), y=fo, fill=Order))+
geom_bar(
width=0.8,
stat="identity",
color = "black",
position="stack",
size =0.3)+
theme_bw()+
xlab("Species")+
ylab("Frequency of occurrence")+
theme(legend.position="top")+
theme(axis.text.x = element_text(
angle=45,
vjust=1,
hjust = 1,
family="serif",
face="italic",
colour="black",
size=rel(0.9)))+
geom_text(aes(label=iucn_status),
position=position_dodge(width=0.7),
size=3,
family="serif",
colour="black",
vjust=-0.25)+
theme(plot.margin = unit(c(0.5,0.5,0.5,1),"cm"))
cores<-c("indianred1" , # pH # artiodactyla mudar para indianred #cd5c5c rgb(205,92,92)
"coral", # pH # carnivora #ff7f50 rgb(255,127,80)
"orchid" , # pH # cingulata mudar para orchid
"burlywood", # pH # didelphimorphia #deb887 rgb(222,184,135)
"khaki", # pH # lagomorpha mudar para khaki #f0e68c rgb(240,230,140)
"darkseagreen", # pH # perisodactyla mudar para darkseagreen #8fbc8f rgb(143,188,143)
"mediumaquamarine", # pH # pilosa #66cdaa rgb(102,205,170)
"dodgerblue" ) # pH # rodentia mudar para dodger blue #1e90ff rgb(30,144,255)
#png(filename= "Fig3_v19.png", res= 300, height= 16, width=26, unit="cm")
#p+ scale_fill_manual(values=cores)
#dev.off()
# pH # mesmo que acima, mas usando os codigos
# cores<-c("#cd5c5c", # pH # artiodactyla mudar para indianred #cd5c5c rgb(205,92,92)
# "#ff7f50", # pH # carnivora #ff7f50 rgb(255,127,80)
# "#da70d6", # pH # cingulata mudar para orchid #da70d6 rgb(218,112,214)
# "#deb887", # pH # didelphimorphia #deb887 rgb(222,184,135)
# "#f0e68c", # pH # lagomorpha mudar para khaki #f0e68c rgb(240,230,140)
# "#8fbc8f", # pH # perisodactyla mudar para darkseagreen #8fbc8f rgb(143,188,143)
# "#66cdaa", # pH # pilosa #66cdaa rgb(102,205,170)
# "#1e90ff") # pH # rodentia mudar para dodger blue #1e90ff rgb(30,144,255)
#png(filename= "Fig3_v20.png", res= 300, height= 16, width=26, unit="cm")
#p+ scale_fill_manual(values=cores)
#dev.off()
Fig. 3. Distribution of frequencies of occurrence of the main species evaluated in ATLANTIC-CAMTRAPS, and their status in the 2017 IUCN Red list of threatened species. LC = least concern, NT = near threatened, VU = vulnerable, EN = endangered, CR = critically endangered, DD = data deficient, and IN = invasive species (not an IUCN category).
Generated in ArcGis by Fernando Lima.
Fig. 4. Distribution of taxonomic richness and sampling effort across Atlantic Forest sites where camera traps were used for sampling of medium and large terrestrial mammal species. Opportunistic records (see the text) were removed from this analysis.